This is not really a CQ/AEM question, but a Maven question and should be addressed in such a forum. But, since I actually know the answer, I will hint you on what to do.
I don't know where you have defined your plugin, in the <build> section or the <reporting> section but I assume it is in the <reporting> section as you should. Then you should use the mvn site command.
You could also bind the execution to another goal. Read about Maven lifecyle at [1]. Each Maven plugins has goals that and you can bind your execution to different phases and goals. However... I would strongly advice AGAINST binding the site or javadoc creation to the install phase or any of its goals, since that will force the developers to runt the site/javadoc every time the system is compiled/installed.
Instead, use a Continuous Build tool, such as TeamCity, Hudson, Jenkins or any other, and have that tool build your javadoc and site on each commit instead. Or once every day.
[1] http://maven.apache.org/guides/introduction/introduction-to-the-lifecycle.html